combine_predict_grid: Combine signatures and exposures of different models....

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Combine signatures and exposures of different models. Exposure values are zero for samples in an annotation where that signature was not predicted

Description

Combine signatures and exposures of different models. Exposure values are zero for samples in an annotation where that signature was not predicted

Usage

combine_predict_grid(
  musica,
  modality,
  signature_res,
  model_ids = NULL,
  result_name = "result",
  model_rename = NULL,
  make_copy = FALSE,
  table_name = NULL
)

Arguments

musica	A musica object.
modality	Modality used for prediction.
signature_res	Signatures to automatically subset from for prediction
model_ids	Vector of ids for the models to combine. If null, all models in the modality and result_list entry will be combined. Default NULL.
result_name	Name of the result list entry containing the signatures to plot. Default "result".
model_rename	New model identifier. If null, will be combination of the ids for the models being combined. Deafult NULL.
make_copy	If FALSE, the inputted musica object is updated and nothing is returned. If TRUE, a new musica object is created and returned. Default FALSE.
table_name	Use modality instead

Value

Returns nothing or a new musica object, depending on the make_copy parameter.

Examples

data(musica_annot)
data(cosmic_v2_sigs)
grid <- auto_predict_grid(musica_annot, "SBS96", cosmic_v2_sigs, "lda",
  "Tumor_Subtypes",
  combine_res = FALSE, make_copy = TRUE
)
combined <- combine_predict_grid(grid, "SBS96", cosmic_v2_sigs,
make_copy = TRUE)

campbio/musicatk documentation built on Dec. 25, 2024, 9:34 p.m.